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Sample GSM1059078 Query DataSets for GSM1059078
Status Public on Jan 01, 2016
Title Microaerobic-xylose cy5-2
Sample type RNA
 
Channel 1
Source name Microaerobic-xylose cy5
Organism Ogataea angusta
Characteristics strain: DL-1-L
Extracted molecule total RNA
Extraction protocol To grow the cells aerobically, 500 ml Erlenmeyer flasks containing 50 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and incubated at 37°C while shaking at 180 rpm in an orbital shaker. For microaerobic growth, 250 ml Erlenmeyer flasks containing 100 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and were incubated at 37°C while shaking at 100 rpm in an orbital shaker. Cell growth was monitored by determining the optical density (OD600) with a SHIMADZU UV-2550 Spectrophotometer. The total RNA was extracted by a hot phenol method followed by purification using an RNeasy column kit (Qiagen)
Label cy5
Label protocol 30 µg total RNA of each samples was used for first-strand cDNA synthesis using SuperScript III reverse transcriptase (Invitrogen, USA) with the oligo dT primer. The cDNA labeling was performed using an Aminoallyl post-DNA labeling kit (GeneChem, Korea) following the manufacturer’s protocol with some modifications.
 
Channel 2
Source name Microaerobic-glucose cy3
Organism Ogataea angusta
Characteristics strain: DL-1-L
Extracted molecule total RNA
Extraction protocol To grow the cells aerobically, 500 ml Erlenmeyer flasks containing 50 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and incubated at 37°C while shaking at 180 rpm in an orbital shaker. For microaerobic growth, 250 ml Erlenmeyer flasks containing 100 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and were incubated at 37°C while shaking at 100 rpm in an orbital shaker. Cell growth was monitored by determining the optical density (OD600) with a SHIMADZU UV-2550 Spectrophotometer. The total RNA was extracted by a hot phenol method followed by purification using an RNeasy column kit (Qiagen)
Label cy3
Label protocol 30 µg total RNA of each samples was used for first-strand cDNA synthesis using SuperScript III reverse transcriptase (Invitrogen, USA) with the oligo dT primer. The cDNA labeling was performed using an Aminoallyl post-DNA labeling kit (GeneChem, Korea) following the manufacturer’s protocol with some modifications.
 
 
Hybridization protocol The fluorescent-labeled cDNA was concentrated under a vacuum and resuspended in 15 µl of preheated hybridization buffer (25% formamide, 5x SSC, 0.1% SDS). The pairs of Cys3 and Cys5-labeled samples were mixed and applied to a post-processing H. polymorpha microarray chip.
Scan protocol After incubation in the dark at 42°C for 16 – 18 h, the slide was washed, dried, and scanned for Cy5(635 nm) and Cy3(532 nm) signals using a GenePix4000B scanner (Axon Instruments)
Description The transcriptomes of Hansenula polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions
Data processing Spot identification and fluorescent signal quantitation were conducted using GenePix Pro v6.0 software, where any flagged, not found, saturated, or bad signal spot was automatically and manually eliminated.
Data processing and normalization were performed with the Arraynorm program. This data has the Matrix worksheet in your submission contains the normalized data that was generated by the Arraynorm software.
 
Submission date Jan 02, 2013
Last update date Jan 01, 2016
Contact name Oh Cheol Kim
E-mail(s) kill572@kribb.re.kr
Organization name KRIBB
Street address Gwahakro 125
City Daejeon
ZIP/Postal code 82
Country South Korea
 
Platform ID GPL16437
Series (1)
GSE43240 Transcriptome analysis of xylose metabolism in the methylotrophic yeast Hansenula polymopha

Data table header descriptions
ID_REF
VALUE log2 'xylose/glucose'

Data table
ID_REF VALUE
KH-6132
KH-6133 0.07
KH-6134 -0.46
KH-6135 -0.08
KH-6116 1.08
KH-6117 -0.27
KH-6118 -0.40
KH-6119 -0.17
KH-6099 -0.20
KH-6100 0.09
KH-6101 -0.47
KH-6102 0.36
KH-6083 -0.04
KH-6084 0.19
KH-6085
KH-6086 0.11
KH-6067 0.25
KH-6068 -0.70
KH-6069
KH-6070 0.68

Total number of rows: 5838

Table truncated, full table size 75 Kbytes.




Supplementary file Size Download File type/resource
GSM1059078_Final_X100_cy5-2.gpr.gz 555.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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